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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2185/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TransView 1.50.0  (landing page)
Julius Muller
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/TransView
git_branch: RELEASE_3_20
git_last_commit: 21d33cd
git_last_commit_date: 2024-12-12 03:54:15 -0500 (Thu, 12 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


INSTALL results for TransView on nebbiolo2

To the developers/maintainers of the TransView package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TransView
Version: 1.50.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TransView
StartedAt: 2024-12-19 15:14:33 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 15:14:48 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 15.7 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TransView
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_density.c -o bin_density.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c construct_dc.c -o construct_dc.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts.h:36,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/sam.h:33,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/samtools-1.7-compat.h:5,
                 from parse_sam.h:4,
                 from construct_dc.c:23:
/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts_log.h:76:1: warning: ‘Rprintf’ is an unrecognized format function type [-Wformat=]
   76 | HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);
      | ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c parse_sam.c -o parse_sam.o
parse_sam.c: In function ‘quality_check’:
parse_sam.c:161:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                          ~^                                 ~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |                                                |
      |                                                                           int                                              hts_pos_t {aka long int}
      |                                                                          %ld
parse_sam.c:161:103: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘uint32_t *’ {aka ‘unsigned int *’} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                                                      ~^
      |                                                                                                       |
      |                                                                                                       int
      |                                                                                                      %ls
parse_sam.c: In function ‘print_readinfo’:
parse_sam.c:202:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  202 |         printf("Pos %d\n",current_read->core.pos);
      |                     ~^    ~~~~~~~~~~~~~~~~~~~~~~
      |                      |                      |
      |                      int                    hts_pos_t {aka long int}
      |                     %ld
parse_sam.c:203:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  203 |         printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
      |                                ~^                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                 |                                   |
      |                                 int                                 hts_pos_t {aka long int}
      |                                %ld
parse_sam.c: In function ‘seq_density’:
parse_sam.c:314:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %ld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
      |                                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                       |
      |                                                                       hts_pos_t {aka long int}
parse_sam.c:314:94: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                                                             ~^
      |                                                                                              |
      |                                                                                              int
      |                                                                                             %ld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
  316 |                                         current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                              |
      |                                                                              hts_pos_t {aka long int}
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c slice_dc.c -o slice_dc.o
slice_dc.c: In function ‘slice_dc’:
slice_dc.c:184:33: warning: ‘slicep’ may be used uninitialized [-Wmaybe-uninitialized]
  184 |                                 expand(slicep,new_vecp,rebuildc,wsize);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
slice_dc.c:101:22: note: ‘slicep’ was declared here
  101 |                 int *slicep= INTEGER_POINTER(slice);
      |                      ^~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c visuals.c -o visuals.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-TransView/00new/TransView/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TransView)